import matplotlib.pyplot as plt
import numpy as np
from math import sqrt, acos, sin

D_kcal = 100 # kcal/mol
n = 55 # 1/nm
r_e = 1. #nm - equilibrium distance
D_en = D_kcal*4184e9 # from kcal to N*nm
mol = 6.022e-23 # 1 atom

X_aHem_2d = np.array([[2.16, 0.0],
                      [2.77, -0.19],
                      [3.24, -0.1 ],
                      [3.59, -0.1 ],
                      [3.83, -0.35],
                      [3.84, -0.8 ],
                      [3.67, -1.34],
                      [3.73, -1.96],
                      [3.93, -2.31],
                      [4.23, -2.67],
                      [4.44, -2.81],
                      [4.33, -3.25],
                      [4.01, -3.5 ],
                      [3.99, -3.67],
                      [4.11, -3.94],
                      [4.39, -4.12],
                      [4.44, -4.52],
                      [4.73, -4.86],
                      [4.96, -5.41],
                      [4.89, -5.87],
                      [4.63, -6.44],
                      [4.43, -6.96],
                      [4.07, -7.32],
                      [3.71, -7.51],
                      [3.46, -7.36],
                      [3.41, -7.1 ],
                      [3.31, -6.9 ],
                      [3.04, -6.87],
                      [2.73, -6.73],
                      [2.41, -6.6 ],
                      [2.17, -6.41],
                      [1.97, -6.23],
                      [1.84, -6.03],
                      [1.76, -5.87],
                      [1.54, -5.87],
                      [1.4 , -5.96],
                      [1.31, -6.16],
                      [1.39, -6.57],
                      [1.6 , -6.81],
                      [1.71, -7.09],
                      [1.76, -7.32],
                      [1.67, -7.65],
                      [1.44, -7.81],
                      [1.49, -8.06],
                      [1.56, -8.36],
                      [1.44, -8.61],
                      [1.43, -8.79],
                      [1.44, -9.1 ],
                      [1.6 , -9.48],
                      [1.74, -9.84],
                      [1.63, -10.0],
                      [1.47, -10.19],
                      [1.26, -10.21],
                      [1.07, -10.05],
                      [1.03, -9.76],
                      [1.09, -9.44],
                      [1.07, -9.02],
                      [0.86, -8.79],
                      [0.64, -8.68],
                      [0.63, -8.36],
                      [0.8 , -8.22],
                      [0.81, -7.93],
                      [0.89, -7.71],
                      [1.04, -7.51],
                      [1.1 , -7.25],
                      [0.91, -7.02],
                      [0.91, -6.76],
                      [0.91, -6.48],
                      [0.69, -6.25],
                      [0.69, -6.  ],
                      [0.66, -5.68],
                      [0.59, -5.36],
                      [0.53, -5.12],
                      [0.54, -4.92],
                      [0.79, -4.84],
                      [1.03, -4.89],
                      [1.21, -4.7 ],
                      [1.36, -4.42],
                      [1.49, -4.16],
                      [1.66, -3.92],
                      [1.66, -3.7 ],
                      [1.8 , -3.41],
                      [2.  , -3.22],
                      [1.91, -2.93],
                      [1.8 , -2.71],
                      [1.56, -2.55],
                      [1.46, -2.38],
                      [1.3 , -2.19],
                      [1.21, -1.93],
                      [1.09, -1.64],
                      [0.9 , -1.45],
                      [0.8 , -1.28],
                      [0.84, -1.  ],
                      [1.  , -0.8 ],
                      [1.26, -0.64],
                      [1.7 , -0.31]])

